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pom.xml
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pom.xml
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>uk.ac.liv</groupId>
<artifactId>mzidlib</artifactId>
<version>1.7</version>
<packaging>jar</packaging>
<name>mzidlib</name>
<url>https://github.com/fghali/mzidlib/</url>
<description>MzidLib - A library of routines for manipulating data in the PSI's mzIdentML standard. ProteoAnnotator is a completely automated software pipeline for integration of mass spectrometry (MS) based proteomic evidence into genome databases. http://www.proteoannotator.org/ </description>
<licenses>
<license>
<name>The Apache License, Version 2.0</name>
<url>http://www.apache.org/licenses/LICENSE-2.0.txt</url>
</license>
</licenses>
<developers>
<developer>
<name>Fawaz Ghali</name>
<id>fawaz</id>
<email>f.ghali@liverpool.ac.uk</email>
<organization>POST-GENOMIC BIOINFORMATICS, Institute of Integrative Biology, University of Liverpool</organization>
</developer>
</developers>
<scm>
<connection>scm:git:git://github.com:fghali/mzidlib.git</connection>
<developerConnection>scm:git:git@github.com:fghali/mzidlib.git</developerConnection>
<url>https://github.com/dser4fghali/mzidlib</url>
<tag>mzidlib-1.7</tag>
</scm>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<parent>
<groupId>org.sonatype.oss</groupId>
<artifactId>oss-parent</artifactId>
<version>9</version>
</parent>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>3.8.1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>uk.ac.ebi.jmzidml</groupId>
<artifactId>jmzidentml</artifactId>
<version>1.2.2</version>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride.tools</groupId>
<artifactId>jmzreader</artifactId>
<version>1.2.0</version>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride.tools</groupId>
<artifactId>mgf-parser</artifactId>
<version>1.2.4</version>
</dependency>
<dependency>
<groupId>uk.ac.ebi.pride.tools</groupId>
<artifactId>mzml-wrapper</artifactId>
<version>1.2</version>
</dependency>
<dependency>
<groupId>uk.ac.ebi.jmzml</groupId>
<artifactId>jmzml</artifactId>
<version>1.6.8</version>
</dependency>
<dependency>
<groupId>de.proteinms.omxparser</groupId>
<artifactId>omssa-parser</artifactId>
<version>1.5.12</version>
</dependency>
<dependency>
<groupId>de.proteinms.xtandemparser</groupId>
<artifactId>xtandem-parser</artifactId>
<version>1.7.7</version>
</dependency>
<dependency>
<groupId>au.com.bytecode</groupId>
<artifactId>opencsv</artifactId>
<version>1.8</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math3</artifactId>
<version>3.2</version>
</dependency>
<dependency>
<groupId>commons-lang</groupId>
<artifactId>commons-lang</artifactId>
<version>2.6</version>
</dependency>
<dependency>
<groupId>commons-collections</groupId>
<artifactId>commons-collections</artifactId>
<version>1.0</version>
</dependency>
<dependency>
<groupId>org.kohsuke.args4j</groupId>
<artifactId>args4j-maven-plugin</artifactId>
<version>2.0.26</version>
</dependency>
</dependencies>
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-release-plugin</artifactId>
<version>2.3.2</version>
<configuration>
<arguments>-Dgpg.passphrase=${gpg.passphrase}</arguments>
</configuration>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.5.1</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<!-- Jar plugin -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.4</version>
<configuration>
<archive>
<manifest>
<addDefaultImplementationEntries>true</addDefaultImplementationEntries>
<addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
<mainClass>uk.ac.liv.mzidlib.MzIdentMLLib</mainClass>
<addClasspath>true</addClasspath>
<classpathPrefix>lib</classpathPrefix>
</manifest>
</archive>
<outputDirectory>${project.build.directory}/${project.artifactId}-${project.version}
</outputDirectory>
</configuration>
</plugin>
<!-- Dependency plugin -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<id>copy-dependencies</id>
<phase>package</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<outputDirectory>${project.build.directory}/${project.artifactId}-${project.version}/lib
</outputDirectory>
<overWriteReleases>true</overWriteReleases>
<overWriteSnapshots>true</overWriteSnapshots>
<excludeTransitive>false</excludeTransitive>
</configuration>
</execution>
</executions>
</plugin>
<!-- Resources plugin -->
<plugin>
<artifactId>maven-resources-plugin</artifactId>
<version>2.3</version>
<executions>
<!-- Copy main resources to test resources before testing. -->
<execution>
<id>copy-test-resources</id>
<phase>generate-test-resources</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<overwrite>true</overwrite>
<outputDirectory>src/test/resources</outputDirectory>
<resources>
<resource>
<directory>src/main/resources</directory>
</resource>
</resources>
</configuration>
</execution>
<!-- Copy the resources -->
<execution>
<id>copy-package-resources</id>
<phase>package</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<outputDirectory>${project.build.directory}/${project.artifactId}-${project.version}/
</outputDirectory>
<resources>
<resource>
<directory>./</directory>
<includes>
<include>percolator/</include>
<include>searchgui/</include>
<include>README.txt</include>
<include>ProteoAnnotator_Readme.txt</include>
<include>documentation/MzidLibraryUserGuide.docx</include>
<include>documentation/ProteoAnnotator_user_guide.docx</include>
</includes>
<excludes>
<exclude>documentation</exclude>
<exclude>example_files</exclude>
<exclude>iprg2008_combined</exclude>
<exclude>MzidLib-1.6.zip</exclude>
<exclude>IPeak v1.0.1.zip</exclude>
</excludes>
</resource>
</resources>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-release-plugin</artifactId>
<version>2.3.2</version>
<configuration>
<arguments>-Dgpg.passphrase=${gpg.passphrase}</arguments>
</configuration>
</plugin>
<!-- Pack sources on build -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>2.1.1</version>
<executions>
<execution>
<id>attach-sources</id>
<phase>verify</phase>
<goals>
<goal>jar-no-fork</goal>
</goals>
</execution>
</executions>
</plugin>
<!-- TO BE ADDED: Fawaz<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>2.9.1</version>
<executions>
<execution>
<id>attach-javadocs</id>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
-->
<!-- Assembly plugin -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.2</version> <!-- do not change this version! as this will either ruin the exclusion or the setting of the permission... -->
<configuration>
<descriptors>
<descriptor>src/main/assembly/zip.xml</descriptor>
</descriptors>
</configuration>
<executions>
<execution>
<id>make-assembly</id>
<!-- this is used for inheritance merges -->
<phase>package</phase>
<!-- append to the packaging phase. -->
<goals>
<goal>single</goal>
<!-- goals == mojos -->
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.sonatype.plugins</groupId>
<artifactId>nexus-staging-maven-plugin</artifactId>
<version>1.6.3</version>
<extensions>true</extensions>
<configuration>
<serverId>ossrh</serverId>
<nexusUrl>https://oss.sonatype.org/</nexusUrl>
<autoReleaseAfterClose>true</autoReleaseAfterClose>
</configuration>
</plugin>
</plugins>
<extensions>
<extension>
<groupId>org.jvnet.wagon-svn</groupId>
<artifactId>wagon-svn</artifactId>
<version>1.12</version>
</extension>
</extensions>
</build>
<repositories>
<!-- EBI repo -->
<repository>
<id>nexus-ebi-repo</id>
<name>The EBI internal repository</name>
<url>http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo/</url>
<releases>
</releases>
<snapshots>
<enabled>false</enabled>
</snapshots>
</repository>
<!-- EBI SNAPSHOT repo -->
<repository>
<id>nexus-ebi-snapshot-repo</id>
<name>The EBI internal snapshot repository</name>
<url>http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo-snapshots/</url>
<releases>
<enabled>false</enabled>
</releases>
<snapshots>
</snapshots>
</repository>
<repository>
<id>genesis-maven2-repository</id>
<name>Genesis maven2 repository</name>
<url>http://genesis.UGent.be/maven2</url>
<layout>default</layout>
</repository>
<repository>
<id>maven2-repository.dev.java.net</id>
<name>Java.net Repository for Maven</name>
<url>http://download.java.net/maven/2/</url>
</repository>
</repositories>
<distributionManagement>
<snapshotRepository>
<id>ossrh</id>
<url>https://oss.sonatype.org/content/repositories/snapshots</url>
</snapshotRepository>
<repository>
<id>ossrh</id>
<url>https://oss.sonatype.org/service/local/staging/deploy/maven2/</url>
</repository>
</distributionManagement>
<profiles>
<profile>
<id>release-sign-artifacts</id>
<activation>
<property>
<name>performRelease</name>
<value>true</value>
</property>
</activation>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-gpg-plugin</artifactId>
<version>1.6</version>
<executions>
<execution>
<id>sign-artifacts</id>
<phase>verify</phase>
<goals>
<goal>sign</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
</profiles>
</project>